Comments for O|B|F News

Comment on Dropping Python 2.3 Support by Peter

Peter — Fri, 08 May 2009 20:42:38 +0000

Update: The latest code in CVS/github will no longer install on Python 2.3, and we will gradually start removing any Python 2.3 specific bits of code.

Comment on Biopython and version control systems by Giovanni Marco Dall'Olio

Giovanni Marco Dall'Olio — Tue, 17 Mar 2009 15:13:00 +0000

Thank you for the acknowledgments!!

Let’s see if github will become an useful tool.
Basically it won’t be difficult to keep a copy of the git repository in the open-bio server: maybe, it is not even necessary to have git installed there.

Comment on Julian Lombardi will present keynote at BOSC 2008 by Evolving Bits

Evolving Bits — Mon, 19 May 2008 06:30:20 +0000

Julian Lombardi will speak at BOSC

As has been announced recently on the home page of this year’s BOSC (the Bioinformatics Open Source Conference) and as I just posted on the O|B|F News, Julian Lombardi will be giving the keynote address this year at the conference.
I am serving …

Comment on BioPerl Mailing List Summaries by Chris Fields

Chris Fields — Sat, 24 Jun 2006 14:12:53 +0000

You should be posting this to the mail list and not here:

http://bioperl.org/mailman/listinfo/bioperl-l

BTW, Bio::Tools::Run::Phylo::PAML::Yn00/codeml were recently updated to deal with results from PAML 3.15 which could be your problem, but you’ll have to update from CVS.

Comment on BioPerl Mailing List Summaries by todaewon

todaewon — Sat, 24 Jun 2006 13:38:29 +0000

I just coded according to howto manual
but I can’t get any result. there is no error message~!~

what’s happen??

use lib “/usr/local/lib/perl5/site_perl/5.8.7″;
use Bio::Tools::Run::Phylo::PAML::Yn00;
use Bio::AlignIO;
my $alignio = new Bio::AlignIO(-format => ‘phylip’,
-file => ‘/r1/people/daewon_kim/ Oranutan_cDNA/2.Processing/4.CodonC/dNdSGene1.phylip’,

-idlength=>12,
-interleaved => 1);
my $aln = $alignio->next_aln;

my $yn = new Bio::Tools::Run::Phylo::PAML::Yn00();
$yn->alignment($aln);
my ($rc,$parser) = $yn->run();

if(my $result = $parser->next_result) {
my @otus = $result->get_seqs();
my $MLmatrix = $result->get_MLmatrix();
# 0 and 1 correspond to the 1st and 2nd entry in the @otus array
my $dN = $MLmatrix->[0]->[1]->{dN};
my $dS = $MLmatrix->[0]->[1]->{dS};
my $kaks =$MLmatrix->[0]->[1]->{omega};
print “Ka = $dN Ks = $dS Ka/Ks = $kaks\n”;
}

Comment on mediawiki 1.6.7 by why does frontpage keep trying to install when loading website? » blueabe162

Sun, 11 Jun 2006 14:56:07 +0000

[...] mediawiki 1.6.7 [...]

Comment on Mailing list reading with GMANE by Chris Fields

Chris Fields — Wed, 05 Apr 2006 18:01:04 +0000

I’ll add this to the mailing list for the wiki since using Google seems incomplete and the openbio search is still down.

Comment on sort order for Bio::Tree::Node each_Descendent by Jason Stajich

Jason Stajich — Mon, 27 Feb 2006 14:30:56 +0000

Sounds good – don’t let me stop you from writing it… =)

I think what is best is to add some of these comments to the module page on the wiki when someone has time so we can build a todo list on that page which everyone can edit and update when finished.

Comment on sort order for Bio::Tree::Node each_Descendent by marino

marino — Fri, 24 Feb 2006 21:06:38 +0000

Great job Jason!

I have been trying to order nodes by similarity and the method ‘height’ works very well in most instances. It would be nice to have a ‘revheight’ method as well. I presume that the two methods would be similar to the “Ladderise” left and right from TreeView.

I also think that it would be useful to have a leaf ordering algorithm similar to the one published by Bar-Joseph Z, Gifford DK and Jaakkola TS.Fast optimal leaf ordering for hierarchical clustering. Bioinformatics. 2001;17 Suppl 1:S22-9.

Comment on Discussions about modules that run BLAST by Jason Stajich

Jason Stajich — Tue, 07 Feb 2006 22:37:25 +0000

Fixed them, some sort of weird xhref in link instead of href, maybe javascript was screwed up when I was editing the post.

Also I promoted you to author so you can post news I think.